"Especially for the type of investigation where things are still in motion. The food has been shipped and you may not know where it is. It may be in a truck, on a shelf or in some consumer's pantry, so time really is of the essence," he said.
"Next-generation sequencing tools are available, but these are still too complex and expensive for routine use in the food industry," Brehm-Stecher explained. "New approaches that are able to bridge the gap between the limitations of traditional PCR and next-generation sequencing could enhance food safety efforts by providing both rapid presence/absence testing and detailed genetic characterization of isolates."
You don't have to go further than the local newspaper to see the depth of the problem. Recent national outbreaks of salmonella in foods include peanut butter (2007 and 2009), alfalfa sprouts (2009), black pepper and hydrolyzed vegetable protein (HVP) (2010). Adding to the problem is the fact that peanut butter, black pepper and HVP are all base ingredients used in many other food products. Salmonella in these ingredients has led to thousands of product recalls, hundreds of illnesses and several deaths, Brehm-Stecher said.
The method being developed at Iowa State University starts with a rapid PCR reaction that amplifies a salmonella-specific gene, generating millions of fluorescently labeled copies of this DNA in about 20 minutes.
Next, instead of cycle sequencing, the PCR product is purified for five minutes, SNAP71 (a reagent developed by Advanced Analytical) is added, and the DNA is heated for 10 minutes at 100C.
This reaction chemically cuts the labeled salmonella DNA at all adenine and guanine sites (A's and G's) in the DNA chain.
The result is a complex soup of fluorescently labeled DNA fragments of all sizes.
These fragments are then separated in a high-voltage electric field by
|Contact: Byron Brehm-Stecher|
Iowa State University